|
Status |
Public on Jul 31, 2022 |
Title |
Mouse Embryonic Fibroblasts, replicate 2 |
Sample type |
SRA |
|
|
Source name |
MEF
|
Organism |
Mus musculus |
Characteristics |
cell line: ICR
|
Treatment protocol |
Doxycycline treatment for different time points decribed in each sample. Some samples were treated with LPA as indicated.
|
Growth protocol |
Cell were cultured on MEFs in humdified 5%Co2 , 21% O2 incubator
|
Extracted molecule |
total RNA |
Extraction protocol |
RNeasy mini RNA kit Bulk MARS-seq 3 primed library
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
Mouse Embryonic Fibroblasts, replicate 2
|
Data processing |
Samples were analyzed using UTAP software (Kohen et al. 2019). Reads were trimmed using CutAdapt (Martin 2011) (parameters: -a ADAPTER1 -a “A{10}” -a “T{10}” -A “A{10}” -A “T{10}” –times 2 -u 3 -u -3 -q 20 -m 25). Reads were mapped to genome mm10 using STAR (Dobin et al. 2013) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic - alignSoftClipAtReferenceEnds No). Sample counting was done using STAR, quantifying mm10 RefSeq annotated genes. Further analysis was done for genes having a minimum of five reads in at least one sample. Normalization of the counts and differential expression analysis was performed using DESeq2 (Love et al. 2014) with the parameters betaPrior = true, cooksCutoff = false, and independentFiltering = false. Assembly: mm10
|
|
|
Submission date |
Jun 07, 2022 |
Last update date |
Jul 31, 2022 |
Contact name |
Noa Novershtern |
E-mail(s) |
[email protected]
|
Organization name |
Weizmann Institute of Science
|
Department |
Molecular Genetics
|
Street address |
Weizmann Institute
|
City |
Rehovot |
ZIP/Postal code |
7610001 |
Country |
Israel |
|
|
Platform ID |
GPL24247 |
Series (2) |
GSE205634 |
Ex Utero Development of Post-Gastrulation Synthetic Mouse Embryos Generated Solely from Naïve Pluripotent Stem Cells [RNA-seq] |
GSE208681 |
Ex Utero Development of Post-Gastrulation Synthetic Embryos Generated Solely from Naïve Pluripotent Stem Cells |
|
Relations |
BioSample |
SAMN28901943 |
SRA |
SRX15625549 |